Deep-tissue transcriptomics and subcellular imaging at high spatial resolution.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 39977545.
- Also identified by DOI 10.1126/science.adq2084 and PMC identifier 12005972.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. We introduce cycle hybridization chain reaction (cycleHCR), a method that integrates multicycle DNA barcoding with HCR to overcome this limitation. cycleHCR enables highly multiplexed imaging of RNA and proteins using a unified barcode system. Whole-embryo transcriptomics imaging achieved precise three-dimensional gene expression and cell fate mapping across a specimen depth of ~310 μm. When combined with expansion microscopy, cycleHCR revealed an intricate network of 10 subcellular structures in mouse embryonic fibroblasts. In mouse hippocampal slices, multiplex RNA and protein imaging uncovered complex gene expression gradients and cell-type-specific nuclear structural variations. cycleHCR provides a quantitative framework for elucidating spatial regulation in deep tissue contexts for research and has potential diagnostic applications.
Medical subject headings
- Gene Expression Profiling
- Microscopy, Fluorescence
- Molecular Imaging
- RNA
- In Situ Hybridization, Fluorescence